Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Marcus D. Wilson,David S. Rueda,Valerie E. Pye,Peter Cherepanov,Ludovic Renault,Daniel P. Maskell,Alessandro Costa,Andrea Nans,Mohamed Ghoneim

doi:10.1038/s41467-019-12007-w

Abstract

Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.

Highlights

Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA
We employ a combination of cryo-EM and singlemolecule Förster resonance energy transfer (FRET) assay to understand what impact retroviral integration has on the structure of the target nucleosome core particle (NCP)
Over the last 35 years macromolecular crystallography has provided several high-resolution views of the NCP and its binding partners. These efforts led to describing the NCP architecture at an atomic level[7,8,9], explained how DNA sequence can influence wrapping of the double helix[35], and how common docking sites on the histone octamer are recognised by different interactors[36,37,38,39,40]

Summary

Introduction

Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. Despite the modest level of detail, the cryo-EM data revealed that intasome induces the sharp bending of the nucleosomal DNA by lifting it off the face of the histone octamer at the site of integration. Due to the limited resolution of the original structure, it was impossible to visualise the conformational rearrangements in the nucleosomal DNA that lead to its disengagement from the nucleosomal core at the site of integration It remains to be established whether nucleosomal DNA deformation at the integration site is merely accommodated by local deformation of the duplex DNA structure, or it rather involves global repositioning of the nucleosomal DNA along the histone octamer. With our findings we uncover unexpected similarities between the mechanisms of retroviral integration and ATP-dependent chromatin remodelling[21,22,23]

Methods

Results

Conclusion